On Thu, Sep 15, 2016, Mochena, Mogus D. wrote:
> I am trying to simulate a double - stacked beta sheet that involves
> thousands of atoms. It has repeating units in it, except for minor
> modifications at the boundaries. Instead of calculating the thousands of
> atoms of something repeating, I wanted to idealize the system, i.e make
> it infinite in size, so that I could use a unit cell or supercell with
> much fewer atoms.
Amber doesn't support infinite chains: there cannot be covalent bonds between
atoms in different unit cells.
I'm pretty sure CHARMM avoids this limitation; don't know about other MD
programs. Since you are planning to do QM, you might consider periodic QM
codes--depends on how many atoms are really in your repeating unit.
...dac
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Received on Fri Sep 16 2016 - 02:30:04 PDT
